|
| Status |
Public on Mar 30, 2018 |
| Title |
PM1 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle
|
| Organism |
Ovis aries |
| Characteristics |
muscle: Psoas major
animal: cross-bred lamb
id animal: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified with TRIzol® Reagent in conjunction with PureLink RNA Mini Kit. To avoid genomic DNA contamination, eluted RNA was treated with DNase-free DNase Set (QIAGEN). RNA yield and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Libraries from individual samples were sequenced with Illumina's HiSeq 2000 at Macrogen (Korea) using 100-pb paired-end sequencing reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to the reference genome (Oar_v3.1) using the software package Tophat (v2.0.13).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.2.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.2.1) was used for merging together each of the assemblies with the reference ovine annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Sheep genome assembly: Oar_v3.1
Supplementary_files_format_and_content: Text files including locus, chromosome location, gene name, and number of mapped reads
|
| |
|
| Submission date |
Mar 29, 2018 |
| Last update date |
Mar 30, 2018 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
fpenagarican@wisc.edu
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Animal and Dairy Sciences
|
| Street address |
1675 Observatory Drive
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL15670 |
| Series (1) |
| GSE112500 |
Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq |
|
| Relations |
| BioSample |
SAMN08814554 |
| SRA |
SRX3864002 |
